Oncology NGS Report v.2.0

For research use only

Sample: syn3-normal

Project: bcbio postproc dream chr21, hg19
not generated Patient: unknown
Coverage interval: regional, total size 1678843 bp

Mutations Alterations in actionable genes Circos plot Seq2C log2 ratios (CNV) Coverage analysis

Mutations

No variants detected.

Actionable genes - variants and larger alterations of interest

No variations found in actionable genes.

Circos plot

Circos plot displays the following genomic data: CNVs, SNPs and structural variants. The outer ring indicates the chromosomes and distances in Mb. The next ring indicates the copy number information. Color scheme correspond to Seq2C plot colors.

The innermost ring represents CNV according to Seq2C: amplifications and deletions in key genes, amplifications and deletions in other genes. Vertical offset represents the log ratio of the gene coverage.

SNP track represents the allele frequency of the SNPs (from 0 to 100%), classes are represented by color: known, likely, unknown (in key genes); known, likely, unknown (in other genes). Vertical offset represents allele frequency of the SNPs (from 0 to 100%).

Archs represent chromosomal rearrangements.

Click on the chromosome header to zoom into a chromosome. Compare all samples

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Seq2C log2 ratios (CNV)

No Seq2C events found.

Coverage analysis for 300 key genes

Height indicates gene average coverage, green means that > 90% gene is covered at 37x (half of global average coverage). More detailed plot for each gene is expanded by clicking on the corresponding point.

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"ENST00000475779", "ENST00000497305", "ENST00000466812", "ENST00000400501", "ENST00000563121", "ENST00000467764", "ENST00000582361", "ENST00000481230", "ENST00000491623", "ENST00000543255", "ENST00000465581", "ENST00000546983", "ENST00000485180", "ENST00000497222", "ENST00000420577", "ENST00000583932", "ENST00000478546", "ENST00000544103", "ENST00000461706", "ENST00000264033", "ENST00000433483", "ENST00000557648", "ENST00000509765", "ENST00000428014", "ENST00000451331", "ENST00000324803", "ENST00000482838", "ENST00000303577", "ENST00000587328", "ENST00000396043", "ENST00000469894", "ENST00000523260", "ENST00000403336", "ENST00000466738", "ENST00000459743", "ENST00000461014", "ENST00000585978", "ENST00000412450", "ENST00000498907", "ENST00000537057", "ENST00000514164", "ENST00000591106", "ENST00000527181", "ENST00000503591", "ENST00000553736", "ENST00000459774", "ENST00000477947", "ENST00000334134", "ENST00000480323", "ENST00000484879", "ENST00000384835", "ENST00000566078", "ENST00000485503", "ENST00000540499", "ENST00000469188", "ENST00000590776", "ENST00000533776", "ENST00000585465", "ENST00000456729", "ENST00000462255", "ENST00000442430", "ENST00000560704", "ENST00000330315", "ENST00000470206", "ENST00000497519", "ENST00000485914", "ENST00000497090", "ENST00000596221", "ENST00000508084", "ENST00000452382", "ENST00000462899", "ENST00000543390", "ENST00000347978", "ENST00000462687", "ENST00000414174", "ENST00000465335", "ENST00000556251", "ENST00000482021", "ENST00000307940", "ENST00000586253", "ENST00000518057", "ENST00000343677", "ENST00000561317", "ENST00000589214", "ENST00000541118", "ENST00000429009", "ENST00000519469", "ENST00000482101", "ENST00000391791", "ENST00000512959", "ENST00000482622", "ENST00000532781", "ENST00000397789", "ENST00000556131", "ENST00000403284", "ENST00000464710", "ENST00000498339", "ENST00000513736", "ENST00000568255", "ENST00000460207", "ENST00000507148", "ENST00000237837", "ENST00000472832", "ENST00000599284", "ENST00000498026", "ENST00000479509", "ENST00000439640", "ENST00000371761", "ENST00000512566", "ENST00000484556", "ENST00000442489", "ENST00000450953", "ENST00000552054", "ENST00000539357", "ENST00000479423", "ENST00000406659", "ENST00000486748", "ENST00000541542", "ENST00000462537", "ENST00000469930", "ENST00000461472", "ENST00000586308", "ENST00000468052", "ENST00000411960", "ENST00000359033", "ENST00000574121", "ENST00000370800", "ENST00000476059", "ENST00000488981", "ENST00000338270", "ENST00000512381", "ENST00000561962", "ENST00000586921", "ENST00000604095", "ENST00000581582", "ENST00000380381", "ENST00000491250", "ENST00000498037", "ENST00000488282", "ENST00000551425", "ENST00000495775", "ENST00000491649", "ENST00000605656", "ENST00000512258", "ENST00000555564", "ENST00000527775", "ENST00000380874", "ENST00000498122", "ENST00000473292", "ENST00000539462", "ENST00000536783", "ENST00000263253", "ENST00000397006", "ENST00000547853", "ENST00000475602", "ENST00000527848", "ENST00000424867", "ENST00000434194", "ENST00000518208", "ENST00000566326", "ENST00000400790", "ENST00000542565", "ENST00000496382", "ENST00000490179", "ENST00000413998", "ENST00000503413", "ENST00000524204", "ENST00000587061", "ENST00000294312", "ENST00000470173", "ENST00000469068", "ENST00000581055", "ENST00000513107", "ENST00000467863", "ENST00000562118", "ENST00000444261", "ENST00000258829", "ENST00000569110", "ENST00000492690", "ENST00000508832", "ENST00000550388", "ENST00000573163", "ENST00000415839", "ENST00000478647", "ENST00000489037", "ENST00000487688", "ENST00000480571", "ENST00000487310", "ENST00000371244", "ENST00000411677", "ENST00000509953", "ENST00000265538", "ENST00000377115", "ENST00000547610", "ENST00000433757", "ENST00000481256", "ENST00000475698", "ENST00000340398", "ENST00000540425", "ENST00000558569", "ENST00000520751", "ENST00000467323", "ENST00000495499", "ENST00000591301", "ENST00000411819", "ENST00000562239", "ENST00000479913", "ENST00000466825", "ENST00000606261", "ENST00000464011", "ENST00000601941", "ENST00000536413", "ENST00000565264", "ENST00000494014", "ENST00000542367", "ENST00000531765", "ENST00000591039", "ENST00000558240", "ENST00000599513", "ENST00000475610", "ENST00000491111", "ENST00000228837", "ENST00000520550", "ENST00000528293", "ENST00000491636", "ENST00000359450", "ENST00000507786", "ENST00000471046", "ENST00000309334", "ENST00000444034", "ENST00000467480", "ENST00000507536", "ENST00000577913", "ENST00000373341", "ENST00000599345", "ENST00000421558", "ENST00000539704", "ENST00000477538"], "strands": ["+", "-", "-", "-", "+", "+", "-", "+", "-", "+", "-", "+", "-", "-", "+", "-", "-", "-", "+", "+", "+", "-", "+", "-", "+", "+", "-", "-", "-", "-", "-", "-", "+", "+", "-", "+", "+", "-", "-", "+", "+", "+", "+", "+", "+", "-", "+", "+", "-", "+", "+", "-", "-", "+", "-", "-", "-", "+", "-", "+", "+", "-", "+", "+", "-", "+", "+", "-", "-", "-", "-", "+", "-", "-", "+", "+", "+", "-", "+", "-", "+", "+", "-", "-", "-", "-", "-", "+", "+", "+", "+", "+", "-", "+", "-", "+", "+", "+", "-", "-", "-", "+", "+", "+", "+", "-", "-", "-", "+", "-", "+", "+", "-", "+", "+", "-", "+", "-", "+", "+", "-", "+", "-", "+", "-", "+", "+", "+", "+", "+", "-", "+", "+", "+", "-", "-", "-", "-", "+", "-", "-", "+", "+", "-", "+", "-", "-", "-", "-", "+", "+", "+", "-", "+", "+", "-", "-", "+", "+", "+", "+", "-", "-", "-", "+", "+", "+", "+", "-", "+", "-", "+", "+", "-", "-", "-", "+", "-", "-", "+", "+", "-", "+", "+", "-", "-", "-", "+", "+", "+", "+", "+", "-", "+", "+", "-", "-", "-", "-", "-", "-", "-", "+", "-", "+", "+", "+", "-", "+", "+", "+", "-", "-", "+", "-", "-", "+", "+", "-", "-", "+", "+", "+", "-", "+", "-", "+", "+", "+", "+", "-", "-", "+", "-", "-", "-", "+", "+", "-", "+", "-", "+", "-", "+", "-", "+", "-", "-", "-", "+", "+", "-", "+", "-", "-", "-", "+", "+", "+", "-", "-", "-", "+", "+", "+", "+", "+", "+", "+", "-", "+", "-", "-", "+", "-", "+", "+", "+", "-", "+", "-", "+", "-", "-", "+", "-", "-", "-", "-", "+", "+", "+", "+", "+", "-", "-", "-", "-", "+", "+"]}

Gene	Chr	Depth	% cov at 37x
ABL1	9	0	0
ACVR1B	12	0	0
ACVR2A	2	0	0
ACVRL1	12	0	0
AGTR2	X	0	0
AJUBA	14	0	0
AKT1	14	0	0
AKT1S1	19	0	0
AKT2	19	0	0
AKT3	1	0	0
ALK	2	0	0
AMER1	X	0	0
APC	5	0	0
AR	X	0	0
ARAF	X	0	0
ARHGAP35	19	0	0
ARID1A	1	0	0
ARID1B	6	0	0
ARID2	12	0	0
ARID5B	10	0	0
ASXL1	20	0	0
ATM	11	0	0
ATR	3	0	0
ATRX	X	0	0
AXIN2	17	0	0
B4GALT3	1	0	0
BAP1	3	0	0
BCL2L1	20	0	0
BCL9	1	0	0
BRAF	7	0	0
BRCA1	17	0	0
BRCA2	13	0	0
BRD2	6	0	0
BRD3	9	0	0
BRD4	19	0	0
BRD9	5	0	0
BRIP1	17	0	0
CBFB	16	0	0
CBL	11	0	0
CCND1	11	0	0
CCND2	12	0	0
CCND3	6	0	0
CCNE1	19	0	0
CDH1	16	0	0
CDK12	17	0	0
CDK4	12	0	0
CDK6	7	0	0
CDK8	13	0	0
CDK9	9	0	0
CDKN1A	6	0	0
CDKN1B	12	0	0
CDKN2A	9	0	0
CDKN2B	9	0	0
CDKN2C	1	0	0
CEBPA	19	0	0
CHEK1	11	0	0
CHEK2	22	0	0
CRIPAK	4	0	0
CRKL	22	0	0
CSNK2A1	20	0	0
CTCF	16	0	0
CTNNB1	3	0	0
CYP2D6	22	0	0
DCUN1D1	3	0	0
DDR1	6	0	0
DDR2	1	0	0
DEPTOR	8	0	0
DNMT3A	2	0	0
EGFR	7	0	0
EGR3	8	0	0
EIF4A2	3	0	0
ELF3	1	0	0
EP300	22	0	0
EPHA3	3	0	0
EPHB6	7	0	0
EPPK1	8	0	0
ERAS	X	0	0
ERBB2	17	0	0
ERBB3	12	0	0
ERBB4	2	0	0
ERCC1	19	0	0
ERCC2	19	0	0
ERRFI1	1	0	0
ESR1	6	0	0
EZH2	7	0	0
FAM175A	4	0	0
FBXW7	4	0	0
FGF1	5	0	0
FGF10	5	0	0
FGF12	3	0	0
FGF14	13	0	0
FGF19	11	0	0
FGF2	4	0	0
FGF23	12	0	0
FGF3	11	0	0
FGF4	11	0	0
FGF5	4	0	0
FGF6	12	0	0
FGF7	15	0	0
FGF8	10	0	0

Gene	Chr	Depth	% cov at 37x
FGF9	13	0	0
FGFR1	8	0	0
FGFR2	10	0	0
FGFR3	4	0	0
FGFR4	5	0	0
FKBP1A	20	0	0
FLT3	13	0	0
FOXA1	14	0	0
FOXA2	20	0	0
FOXC1	6	0	0
FOXL2	3	0	0
FRS2	12	0	0
GAS6	13	0	0
GATA3	10	0	0
GNA11	19	0	0
GNA13	17	0	0
GNAQ	9	0	0
GNAS	20	0	0
H3F3C	12	0	0
HGF	7	0	0
HIST1H1C	6	0	0
HIST1H2BD	6	0	0
HNF1A	12	0	0
HRAS	11	0	0
IDH1	2	0	0
IDH2	15	0	0
IGF1R	15	0	0
IL6	7	0	0
INPP4A	2	0	0
INPP4B	4	0	0
IRAK4	12	0	0
JAK1	1	0	0
JAK2	9	0	0
JAK3	19	0	0
KDM5C	X	0	0
KDM6A	X	0	0
KDR	4	0	0
KEAP1	19	0	0
KIT	4	0	0
KMT2B	19	0	0
KMT2C	7	0	0
KMT2D	12	0	0
KRAS	12	0	0
LAMP1	13	0	0
LIFR	5	0	0
LRRK2	12	0	0
MALAT1	11	0	0
MAP2K1	15	0	0
MAP2K2	19	0	0
MAP2K4	17	0	0
MAP3K1	5	0	0
MAP3K13	3	0	0
MAP3K8	10	0	0
MAPK1	22	0	0
MAPK3	16	0	0
MAPK8IP1	11	0	0
MAPKAP1	9	0	0
MCL1	1	0	0
MDM2	12	0	0
MDM4	1	0	0
MECOM	3	0	0
MED12	X	0	0
MET	7	0	0
MGA	15	0	0
MIR142	17	0	0
MITF	3	0	0
MLH1	3	0	0
MLH3	14	0	0
MLST8	16	0	0
MPL	1	0	0
MRAS	3	0	0
MSH2	2	0	0
MSH3	5	0	0
MSH6	2	0	0
MTOR	1	0	0
MUTYH	1	0	0
MYC	8	0	0
MYCL	1	0	0
MYCN	2	0	0
MYH9	22	0	0
NAV3	12	0	0
NCOR1	17	0	0
NCOR2	12	0	0
NF1	17	0	0
NF2	22	0	0
NFE2L2	2	0	0
NFE2L3	7	0	0
NKX2-1	14	0	0
NKX2-8	14	0	0
NOTCH1	9	0	0
NPM1	5	0	0
NRAS	1	0	0
NRG1	8	0	0
NSD1	5	0	0
PAK1	11	0	0
PALB2	16	0	0
PBRM1	3	0	0
PCBP1	2	0	0
PDGFRA	4	0	0
PDPK1	16	0	0

Gene	Chr	Depth	% cov at 37x
PHF6	X	0	0
PHLPP1	18	0	0
PHLPP2	16	0	0
PIK3C2B	1	0	0
PIK3C2G	12	0	0
PIK3C3	18	0	0
PIK3CA	3	0	0
PIK3CB	3	0	0
PIK3CD	1	0	0
PIK3CG	7	0	0
PIK3R1	5	0	0
PIK3R2	19	0	0
PIM1	6	0	0
PIM2	X	0	0
PIM3	22	0	0
PMS1	2	0	0
PMS2	7	0	0
POLD1	19	0	0
POLE	12	0	0
POLQ	3	0	0
PPP2R1A	19	0	0
PPP2R2A	8	0	0
PRKAA1	5	0	0
PRKAA2	1	0	0
PRKAB1	12	0	0
PRX	19	0	0
PTCH1	9	0	0
PTEN	10	0	0
PTPN11	12	0	0
PTPN6	12	0	0
RAC1	7	0	0
RAD21	8	0	0
RAD51B	14	0	0
RAD51C	17	0	0
RAD51D	17	0	0
RAF1	3	0	0
RASA1	5	0	0
RB1	13	0	0
RBM10	X	0	0
RELN	7	0	0
RET	10	0	0
RHEB	7	0	0
RHOA	3	0	0
RICTOR	5	0	0
RIT1	1	0	0
ROS1	6	0	0
RPL22	1	0	0
RPL5	1	0	0
RPS6	9	0	0
RPS6KB1	17	0	0
RPS6KB2	11	0	0
RPTOR	17	0	0
RUNX1	21	0.01	0
SETBP1	18	0	0
SETD2	3	0	0
SF3B1	2	0	0
SGK1	6	0	0
SGK2	20	0	0
SGK3	8	0	0
SHOC2	10	0	0
SIN3A	15	0	0
SMAD2	18	0	0
SMAD4	18	0	0
SMARCA4	19	0	0
SMARCB1	22	0	0
SMC1A	X	0	0
SMC3	10	0	0
SMO	7	0	0
SOS1	2	0	0
SOX17	8	0	0
SOX2	3	0	0
SOX9	17	0	0
SPOP	17	0	0
SPRED1	15	0	0
SRY	Y	0	0
STAG2	X	0	0
STAT3	17	0	0
STK11	19	0	0
TAF1	X	0	0
TBL1XR1	3	0	0
TBX3	12	0	0
TERT	5	0	0
TET2	4	0	0
TFRC	3	0	0
TGFBR2	3	0	0
TIAF1	17	0	0
TLR4	9	0	0
TOP2A	17	0	0
TP53	17	0	0
TSC1	9	0	0
TSC2	16	0	0
TSHZ2	20	0	0
TSHZ3	19	0	0
U2AF1	21	45.08	8460.48 %
USP9X	X	0	0
VEZF1	17	0	0
VHL	3	0	0
WEE1	11	0	0
WT1	11	0	0
ZNF217	20	0	0

Comment mutation